.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH SNP_STORE "1" "June 2017" "snp_store 2.3.1+dfsg-4" "User Commands"
.SH NAME
snp_store \- SnpStore
.PP
SYNOPSIS
.IP
snp_store [OPTIONS] <GENOME FILE> <ALIGNMENT FILE> [<ALIGNMENT FILE> ...]
.PP
DESCRIPTION
.IP
SNP and Indel Calling in Mapped Read Data.
.PP
REQUIRED ARGUMENTS
.IP
GENOME INPUT_FILE
.IP
A reference genome file. Valid filetypes are: .fasta and .fa.
.IP
ALIGNMENTS List of INPUT_FILE's
.IP
Read alignment file(s) sorted by genomic position. Valid filetypes
are: .sam[.*], .gff, and .bam, where * is any of the following
extensions: gz and bgzf for transparent (de)compression.
.PP
OPTIONS
.HP
\fB\-h\fR, \fB\-\-help\fR
.IP
Display the help message.
.HP
\fB\-\-version\-check\fR BOOL
.IP
Turn this option off to disable version update notifications of the
application. One of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO.
Default: 1.
.HP
\fB\-\-version\fR
.IP
Display version information.
.IP
Main Options:
.HP
\fB\-o\fR, \fB\-\-output\fR OUTPUT_FILE
.IP
SNP output file (mandatory). Valid filetype is: .vcf.
.HP
\fB\-osc\fR, \fB\-\-only\-successful\-candidates\fR
.IP
Output only successfully called SNP candidates. Default: Output all
candidates.
.HP
\fB\-dc\fR, \fB\-\-dont\-clip\fR
.IP
Ignore clip tags in gff. Default: off.
.HP
\fB\-mu\fR, \fB\-\-multi\fR
.IP
Keep non\-unique fragmentStore.alignedReadStore. Default: off.
.HP
\fB\-hq\fR, \fB\-\-hide\-qualities\fR
.IP
Only show coverage (no qualities) in SNP output file. Default: off.
.HP
\fB\-sqo\fR, \fB\-\-solexa\-qual\-offset\fR
.IP
Base qualities are encoded as char value \- 64 (instead of char \-
33).
.HP
\fB\-id\fR, \fB\-\-indel\-file\fR OUTPUT_FILE
.IP
Output file for called indels in gff format. Default: off. Valid
filetype is: .gff.
.HP
\fB\-m\fR, \fB\-\-method\fR STRING
.IP
Set method used for SNP calling either threshold based or Maq
method. One of thresh and maq. Default: maq.
.HP
\fB\-mp\fR, \fB\-\-max\-pile\fR INTEGER
.IP
Maximal number of matches allowed to pile up at the same genome
position. In range [1..inf]. Default: 1.
.HP
\fB\-mmp\fR, \fB\-\-merged\-max\-pile\fR
.IP
Do pile up correction on merged lanes. Default: off.
.HP
\fB\-mc\fR, \fB\-\-min\-coverage\fR INTEGER
.IP
Minimal required number of reads covering a candidate position. In
range [1..inf]. Default: 5.
.HP
\fB\-fc\fR, \fB\-\-force\-call\fR INTEGER
.IP
Always call base if count is >= fc, ignore other parameters.
Default: off. In range [1..inf]. Default: 10.
.HP
\fB\-oa\fR, \fB\-\-orientation\-aware\fR
.IP
Distinguish between forward and reverse reads. Default: off.
.HP
\fB\-mpr\fR, \fB\-\-max\-polymer\-run\fR INTEGER
.IP
Discard indels in homopolymer runs longer than mpr. In range
[0..inf]. Default: 100.
.HP
\fB\-dp\fR, \fB\-\-diff\-pos\fR INTEGER
.IP
Minimal number of different read positions supporting the mutation.
In range [0..inf]. Default: 0.
.HP
\fB\-eb\fR, \fB\-\-exclude\-border\fR INTEGER
.IP
Exclude read positions within eb base pairs of read borders for SNV
calling. Default: off. In range [0..inf]. Default: 0.
.HP
\fB\-su\fR, \fB\-\-suboptimal\fR
.IP
Keep suboptimal reads. Default: off
.HP
\fB\-re\fR, \fB\-\-realign\fR
.IP
Realign reads around indel candidates. Default: off
.HP
\fB\-pws\fR, \fB\-\-parse\-window\-size\fR INTEGER
.IP
Genomic window size for parsing reads (concerns memory consumption,
choose smaller windows for higher coverage). In range [1..inf].
Default: 1000000.
.IP
Threshold method related:
.HP
\fB\-mm\fR, \fB\-\-min\-mutations\fR INTEGER
.IP
Minimal number of observed mutations for mutation to be called. In
range [1..inf]. Default: 3.
.HP
\fB\-pt\fR, \fB\-\-perc\-threshold\fR DOUBLE
.IP
Minimal percentage of mutational base for mutation to be called. In
range [0..inf]. Default: 0.25.
.HP
\fB\-mq\fR, \fB\-\-min\-quality\fR DOUBLE
.IP
Minimal average quality of mutational base for mutation to be
called. In range [0..inf]. Default: 10.
.IP
Maq method related:
.HP
\fB\-th\fR, \fB\-\-theta\fR DOUBLE
.IP
Dependency coefficient. In range [0..inf]. Default: 0.85.
.HP
\fB\-hr\fR, \fB\-\-hetero\-rate\fR DOUBLE
.IP
Heterozygote rate. In range [0..1]. Default: 0.001.
.HP
\fB\-mmq\fR, \fB\-\-min\-map\-quality\fR INTEGER
.IP
Minimum base call (mapping) quality for a match to be considered. In
range [0..inf]. Default: 1.
.HP
\fB\-ch\fR, \fB\-\-corrected\-het\fR
.IP
Use amplification bias corrected distribution for heterozygotes.
Default: off.
.HP
\fB\-maf\fR, \fB\-\-mean\-alleleFreq\fR DOUBLE
.IP
Mean ref allele frequency in heterozygotes. In range [0..inf].
Default: 0.51.
.HP
\fB\-ac\fR, \fB\-\-amp\-cycles\fR INTEGER
.IP
Number of amplification cycles. In range [0..inf]. Default: 18.
.HP
\fB\-ae\fR, \fB\-\-amp\-efficiency\fR DOUBLE
.IP
Polymerase efficiency, probability of amplification. In range
[0..1]. Default: 0.3.
.HP
\fB\-in\fR, \fB\-\-initial\-N\fR INTEGER
.IP
Initial allele population size. In range [0..inf]. Default: 10.
.HP
\fB\-mec\fR, \fB\-\-min\-explained\-column\fR DOUBLE
.IP
Minimum fraction of alignment column reads explained by genotype
call. In range [0..1]. Default: 0.8.
.IP
Indel calling options:
.HP
\fB\-it\fR, \fB\-\-indel\-threshold\fR INTEGER
.IP
Minimal number of indel\-supporting reads required for indel calling.
In range [1..inf]. Default: 3.
.HP
\fB\-ipt\fR, \fB\-\-indel\-perc\-threshold\fR DOUBLE
.IP
Minimal ratio of indel\-supporting/covering reads for indel to be
called. In range [0..1]. Default: 0.25.
.HP
\fB\-iqt\fR, \fB\-\-indel\-quality\-thresh\fR INTEGER
.IP
Minimal average quality of inserted base/deletion\-neighboring bases
for indel to be called. In range [0..inf]. Default: 1.
.HP
\fB\-bsi\fR, \fB\-\-both\-strands\-indel\fR
.IP
Both strands need to be observed for indel to be called. Default:
off.
.HP
\fB\-ebi\fR, \fB\-\-exclude\-border\-indel\fR INTEGER
.IP
Same as option \fB\-eb\fR but for indel candidates. In range [0..inf].
Default: 0.
.IP
Other options:
.HP
\fB\-lf\fR, \fB\-\-log\-file\fR STRING
.IP
Write log to FILE.
.HP
\fB\-v\fR, \fB\-\-verbose\fR
.IP
Enable verbose output.
.HP
\fB\-vv\fR, \fB\-\-very\-verbose\fR
.IP
Enable very verbose output.
.HP
\fB\-q\fR, \fB\-\-quiet\fR
.IP
Set verbosity to a minimum.
.PP
EXAMPLES
.IP
snp_store \fB\-mc\fR 2 \fB\-it\fR 2 exampleGenome.fa exampleReads.gff \fB\-o\fR exampleSNPs.vcf \fB\-id\fR exampleIndels.gff
.IP
Call SNPs and indels of a low\-coverage example (minimum coverage and
indel threshold were reduced to 2).
.IP
snp_store \fB\-re\fR \fB\-mc\fR 2 \fB\-it\fR 2 exampleGenome.fa exampleReads.gff \fB\-o\fR exampleSNPs.vcf \fB\-id\fR exampleIndels.gff
.IP
Computes a realignment before variant calling. Now, the two 1bp
insertions should have been merged into one 2bp insertion.
.PP
VERSION
.IP
Last update:
snp_store version: 1.3.6 [tarball]
SeqAn version: 2.3.1